0.016033 0.009257 0.000000 0.000000 0.018514 0.000000 0.000000 0.000000 0.085251 0.000000 0.000000 0.000000 Zhao, M. Liu, C. Sawaya, M.R. Eisenberg, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.000 90.000 120.000 62.370 62.370 11.730 C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking H2 O 18.015 WATER non-polymer C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking Na 1 22.990 SODIUM ION non-polymer C16 H34 O8 354.436 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL POLYETHYLENE GLYCOL PEG4000 non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N C N 7 N O N 8 N O N 9 N O N 10 N H N 11 N H N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N O N 18 N H N 19 N H N 20 N N N 21 S C N 22 N C N 23 N O N 24 N C N 25 N C N 26 N C N 27 N C N 28 N N N 29 N O N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N NA N 46 N O N 47 N C N 48 N C N 49 N O N 50 N C N 51 N C N 52 N O N 53 N C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N O N 59 N C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N C N 66 N C N 67 N O N 68 N C N 69 N C N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N N N 105 S C N 106 N C N 107 N O N 108 N C Y 109 N C Y 110 N C Y 111 N C Y 112 N C Y 113 N C Y 114 N C N 115 N O N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 S C N 129 N C N 130 N O N 131 N C N 132 N O N 133 N O N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N N N 142 S C N 143 N C N 144 N O N 145 N C Y 146 N C Y 147 N C Y 148 N C Y 149 N N Y 150 N C Y 151 N C Y 152 N C Y 153 N C Y 154 N C N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N N N 169 S C N 170 N C N 171 N O N 172 N C Y 173 N C Y 174 N C Y 175 N C Y 176 N C Y 177 N C Y 178 N C N 179 N O N 180 N O N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N doub N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing Y 110 N doub Y 111 N sing Y 112 N sing N 113 N sing Y 114 N doub N 115 N sing Y 116 N doub N 117 N sing Y 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N doub N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing Y 146 N doub Y 147 N sing Y 148 N sing N 149 N sing Y 150 N doub Y 151 N sing Y 152 N sing N 153 N sing Y 154 N sing Y 155 N doub N 156 N sing Y 157 N doub N 158 N sing Y 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing Y 174 N doub Y 175 N sing Y 176 N sing N 177 N sing Y 178 N doub N 179 N sing Y 180 N doub N 181 N sing Y 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 109 20913 20918 10.1073/pnas.1218792109 23213214 Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates. 2012 10.2210/pdb4e0k/pdb pdb_00004e0k 100 1 CCD 2010-12-11 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 0.97911 1.0 137939 0.069 0.970 29973 99.30 24-ID-C APS 0.97911 SYNCHROTRON APS BEAMLINE 24-ID-C 845.918 Amyloidogenic peptide segment KDWSFY 4 syn polymer 354.436 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL 2 syn non-polymer 22.990 SODIUM ION 1 syn non-polymer 18.015 water 49 nat water no no KDWSFY KDWSFY A,B,C,D polypeptide(L) n n n n n n 1 1.95 36.81 VAPOR DIFFUSION, HANGING DROP 6.5 0.1M BIS-TRIS PROPANE pH 6.5, 0.2 M SODIUM FLUORIDE, 20% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 290K 290 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Database references Data collection Database references Derived calculations 1 0 2012-12-19 1 1 2013-06-19 1 2 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2012-03-04 REL REL 0.046 599 98.20 0.060 806 99.80 0.058 949 100.00 0.062 1039 100.00 0.067 1224 100.00 0.071 1286 100.00 0.080 1400 100.00 0.088 1437 100.00 0.102 1599 100.00 0.120 1583 100.00 0.140 1769 100.00 0.144 1788 100.00 0.110 1795 98.50 0.122 1981 99.30 0.147 1944 100.00 0.180 2010 97.90 0.262 2097 98.50 0.340 2173 99.90 0.448 2168 97.40 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL NA SODIUM ION HOH water Synthetic peptide sample PE4 6061 2 PE4 PE4 101 B NA 1 3 NA NA 102 B PE4 6061 2 PE4 PE4 101 C HOH 8 4 HOH HOH 101 A HOH 14 4 HOH HOH 102 A HOH 18 4 HOH HOH 103 A HOH 22 4 HOH HOH 104 A HOH 26 4 HOH HOH 105 A HOH 28 4 HOH HOH 106 A HOH 30 4 HOH HOH 107 A HOH 39 4 HOH HOH 108 A HOH 41 4 HOH HOH 109 A HOH 50 4 HOH HOH 110 A HOH 52 4 HOH HOH 111 A HOH 56 4 HOH HOH 112 A HOH 3 4 HOH HOH 201 B HOH 5 4 HOH HOH 202 B HOH 12 4 HOH HOH 203 B HOH 17 4 HOH HOH 204 B HOH 31 4 HOH HOH 205 B HOH 32 4 HOH HOH 206 B HOH 33 4 HOH HOH 207 B HOH 36 4 HOH HOH 208 B HOH 43 4 HOH HOH 209 B HOH 45 4 HOH HOH 210 B HOH 47 4 HOH HOH 211 B HOH 48 4 HOH HOH 212 B HOH 51 4 HOH HOH 213 B HOH 1 4 HOH HOH 201 C HOH 4 4 HOH HOH 202 C HOH 7 4 HOH HOH 203 C HOH 13 4 HOH HOH 204 C HOH 15 4 HOH HOH 205 C HOH 16 4 HOH HOH 206 C HOH 21 4 HOH HOH 207 C HOH 23 4 HOH HOH 208 C HOH 24 4 HOH HOH 209 C HOH 29 4 HOH HOH 210 C HOH 44 4 HOH HOH 211 C HOH 46 4 HOH HOH 212 C HOH 10 4 HOH HOH 213 C HOH 2 4 HOH HOH 101 D HOH 6 4 HOH HOH 102 D HOH 9 4 HOH HOH 103 D HOH 11 4 HOH HOH 104 D HOH 20 4 HOH HOH 105 D HOH 34 4 HOH HOH 106 D HOH 42 4 HOH HOH 107 D HOH 49 4 HOH HOH 108 D HOH 53 4 HOH HOH 109 D HOH 54 4 HOH HOH 110 D HOH 55 4 HOH HOH 111 D LYS 1 n 1 LYS 1 A ASP 2 n 2 ASP 2 A TRP 3 n 3 TRP 3 A SER 4 n 4 SER 4 A PHE 5 n 5 PHE 5 A TYR 6 n 6 TYR 6 A LYS 1 n 1 LYS 1 B ASP 2 n 2 ASP 2 B TRP 3 n 3 TRP 3 B SER 4 n 4 SER 4 B PHE 5 n 5 PHE 5 B TYR 6 n 6 TYR 6 B LYS 1 n 1 LYS 1 C ASP 2 n 2 ASP 2 C TRP 3 n 3 TRP 3 C SER 4 n 4 SER 4 C PHE 5 n 5 PHE 5 C TYR 6 n 6 TYR 6 C LYS 1 n 1 LYS 1 D ASP 2 n 2 ASP 2 D TRP 3 n 3 TRP 3 D SER 4 n 4 SER 4 D PHE 5 n 5 PHE 5 D TYR 6 n 6 TYR 6 D software_defined_assembly PISA 2 dimeric software_defined_assembly PISA 2 dimeric 890 -9 2030 690 -5 2120 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N ASP 2 A N ASP 2 B O TYR 6 B O TYR 6 C N SER 4 C N SER 4 D O SER 4 D O SER 4 1 B O1 PE4 101 E O1 PE4 1 1 N 1 B C1 PE4 101 E C1 PE4 1 1 N 1 B C2 PE4 101 E C2 PE4 1 1 N 1 B O7 PE4 101 E O7 PE4 1 1 N 1 B C13 PE4 101 E C13 PE4 1 1 N 1 B C14 PE4 101 E C14 PE4 1 1 N 1 B O8 PE4 101 E O8 PE4 1 1 N 1 B C15 PE4 101 E C15 PE4 1 1 N 1 B C16 PE4 101 E C16 PE4 1 1 N 1 C O1 PE4 101 G O1 PE4 1 1 N 1 C C1 PE4 101 G C1 PE4 1 1 N 1 C C2 PE4 101 G C2 PE4 1 1 N 1 C O7 PE4 101 G O7 PE4 1 1 N 1 C C13 PE4 101 G C13 PE4 1 1 N 1 C C14 PE4 101 G C14 PE4 1 1 N 1 C O8 PE4 101 G O8 PE4 1 1 N 1 C C15 PE4 101 G C15 PE4 1 1 N 1 C C16 PE4 101 G C16 PE4 1 1 N 48.940 10.9748 1.730 0.2207 -0.0000 -0.0000 0.2207 -0.0000 -0.4415 0.1311 0.1119 0.1138 0.9700 14.9810 1601 15997 10.0100 99.8400 1.000 0.130 0.9532 0.0600 1 2.010 SIRAS 9.1500 0.7700 0.9000 ML FLAT BULK SOLVENT MODEL 38.5410 0.4070 0.9700 14.9810 49 324 31 0 244 0.010 369 1.417 495 0.095 37 0.009 58 19.613 163 0.1713 0.1495 1.0016 140 1251 1391 11 99.0000 0.1571 0.1342 1.0374 144 1303 1447 11 100.0000 0.1138 0.1072 1.0789 145 1301 1446 11 100.0000 0.1088 0.0908 1.1280 142 1278 1420 11 100.0000 0.1048 0.0891 1.1874 144 1299 1443 11 100.0000 0.1198 0.0941 1.2618 144 1291 1435 11 100.0000 0.1238 0.0961 1.3592 146 1316 1462 11 100.0000 0.1029 0.0982 1.4958 146 1314 1460 11 100.0000 0.1325 0.1003 1.7120 147 1320 1467 11 100.0000 0.1349 0.1075 2.1559 147 1330 1477 11 100.0000 0.1445 0.1304 14.9826 156 1393 1549 11 99.0000 9.162 0.970 14.9810 4E0K -3.000 0.069 1 12.660 99.300 0.448 0.970 1.000 2.420 5383 2168 1 97.400 0.340 1.000 1.020 3.080 5490 2173 1 99.900 0.262 1.020 1.050 3.820 5435 2097 1 98.500 0.180 1.050 1.080 4.890 5364 2010 1 97.900 0.147 1.080 1.120 5.690 5159 1944 1 100.000 0.122 1.120 1.160 6.680 5411 1981 1 99.300 0.110 1.160 1.200 7.220 5033 1795 1 98.500 0.144 1.200 1.250 9.170 9045 1788 1 100.000 0.140 1.250 1.310 11.090 11764 1769 1 100.000 0.120 1.310 1.370 13.160 10607 1583 1 100.000 0.102 1.370 1.450 15.660 10676 1599 1 100.000 0.088 1.450 1.530 18.100 9680 1437 1 100.000 0.080 1.530 1.640 20.790 9283 1400 1 100.000 0.071 1.640 1.770 23.720 8510 1286 1 100.000 0.067 1.770 1.940 26.120 8047 1224 1 100.000 0.062 1.940 2.170 29.010 6712 1039 1 100.000 0.058 2.170 2.510 29.890 6277 949 1 100.000 0.060 2.510 3.070 31.340 5165 806 1 99.800 0.046 3.070 4.340 31.900 3330 599 1 98.200 0.043 4.340 31.180 1568 326 1 95.000 data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.7_650 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2 Microglobulin (58-63) 1 N N 1 N N 1 N N 1 N N 2 N N 3 N N 2 N N 4 N N 4 N N 4 N N 4 N N metalc 2.831 B B ASP 2 B OD1 ASP 2 1_555 B NA 102 F NA NA 1_555 PROTEIN FIBRIL amyloid, out-of-register, fiber-forming, PROTEIN FIBRIL 4E0K PDB 1 4E0K 1 6 4E0K 1 6 4E0K A 1 1 6 1 6 4E0K 1 6 4E0K B 1 1 6 1 6 4E0K 1 6 4E0K C 1 1 6 1 6 4E0K 1 6 4E0K D 1 1 6 2 2 anti-parallel anti-parallel A ASP 2 A ASP 2 A PHE 5 A PHE 5 B TRP 3 B TRP 3 B TYR 6 B TYR 6 C TRP 3 C TRP 3 C PHE 5 C PHE 5 D TRP 3 D TRP 3 D PHE 5 D PHE 5 BINDING SITE FOR RESIDUE PE4 B 101 B PE4 101 Software 14 BINDING SITE FOR RESIDUE NA B 102 B NA 102 Software 5 BINDING SITE FOR RESIDUE PE4 C 101 C PE4 101 Software 10 A TRP 3 A TRP 3 14 6_555 A TYR 6 A TYR 6 14 1_556 A HOH 103 H HOH 14 6_555 B TRP 3 B TRP 3 14 6_555 B PHE 5 B PHE 5 14 6_554 B TYR 6 B TYR 6 14 1_555 B HOH 203 I HOH 14 1_555 B HOH 207 I HOH 14 1_555 B HOH 208 I HOH 14 1_556 B HOH 208 I HOH 14 1_555 C TRP 3 C TRP 3 14 1_556 C TRP 3 C TRP 3 14 1_555 D TRP 3 D TRP 3 14 1_555 D PHE 5 D PHE 5 14 1_556 A PHE 5 A PHE 5 5 1_556 B ASP 2 B ASP 2 5 1_555 B TRP 3 B TRP 3 5 1_555 D LYS 1 D LYS 1 5 5_554 D HOH 109 K HOH 5 5_554 C TYR 6 C TYR 6 10 3_544 C TYR 6 C TYR 6 10 2_444 C TYR 6 C TYR 6 10 2_445 C HOH 206 J HOH 10 3_544 C HOH 206 J HOH 10 3_543 C HOH 206 J HOH 10 1_554 C HOH 206 J HOH 10 2_444 D TYR 6 D TYR 6 10 3_545 D TYR 6 D TYR 6 10 2_445 D TYR 6 D TYR 6 10 3_544 169 P 61